Viewing AMBER trajectories with dino

This tutorial describes how to view AMBER trajectories with dino.

The files used in this tutorial can be found at:

/sb/apps/dino/examples/binpos

water16.pdb is an AMBER pdb file of this system
water16.trj is a formatted AMBER trajectory
water16.binpos is the binpos version of the trajectory
water16.scr are a script of the dino commands listed above.

  • First, you need an AMBER trajectory. Let's say we have one called water16.trj

  • The next thing you have to do is convert the formatted (ASCII) AMBER trajectory into a binary format called "binpos". There are a few tools that let you do this. The best tool is ptraj. Ptraj documentation can be found in the AMBER manual, or at:

    http://www.chpc.utah.edu/~cheatham/ptraj.html

  • I wrote another crude but simple to use tool called mkbinpos which can do this job. I will describe how to use mkbinpos here.

    mkbinpos reads one or more trajectory files that you specify on the command line and writes them to stdout. Here is mkbinpos usage:

    % mkbinpos
    usage: mkbinpos -n n_atoms [-box] trajectory_files

  • As you can see, in order to use mkbinpos, you need to know the number of atoms in your system and pass it along with the -n option. Also, if your trajectory is of a system in a periodic water box (e.g. a PME calculation), you need to pass the -box option to mkbinpos so that it knows to skip over the box dimension entries found at the end of each frame of the input trajectory files.

    This example system has 6980 atoms. If you don't already know how many atoms your system has, you can get it from several places. I usually get this info from a PDB file that was created from the prmtop file with ambpdb:

    % tail -1 water16.pdb
    ATOM 6980 H2 WAT 491 38.844 25.358 34.021

    From the above we see that the last atom is #6980.

  • This example is a periodic system, so we also have to remember to pass the -box option. Here is the full command to convert water16.trj to water16.binpos:

    % mkbinpos -n 6980 -box water16.trj > water16.binpos
    water16.trj : Using 20940 coordinates (3*6980 atoms) as trajectory frame size
    559 trajectory frames converted to binpos format.

  • If you have several "pieces" of trajectory that you want to stitch together into one binpos file, you can do that easily. Just specify them all in the correct simulation-time order:

    % mkbinpos -n 6980 -box 1.trj 2.trj 3.trj > all.binpos

  • Now you have the binpos format trajectory file and are ready to start dino...

    % dino

    Welcome to dino v0.8.5-1 (http://www.dino3d.org)

    Graphics Subsystem ID: NVIDIA Corporation Quadro2 MXR/AGP/3DNOW!
    OpenGL Version 1.3

    dino> load water16.pdb // load a pdb file corresponding to this trajectory
    dino> .water16 load water16.binpos // load the trajectory
    dino> .water16 new -name all // create object
    dino> scene center [.water16] // center object
    dino> scene autoslab // set slab
    dino> .water16 play // start playback. Other commands are 'step' and 'stop'

  • That's it! You should have the trajectory playing in the dino window, rendered as lines. You can do some more fancy rendering, too, but it may require a script to update the display of the solid objects. For example if you had the CA trace rendered as hsc and wanted to view the trajectory of that: 
    .water16.ca render
.water16 step
.water16.ca render
.water16 step
.water16.ca render
.water16 step
...
...
...
    Put many such commands in a script and that would emulate playing back the solid rendered objects, too. My understanding is that this behavior may be fixed in future versions of dino so that this workaround for solid rendered objects wouldn't be necessary.